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drawtree.yaml
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drawtree.yaml
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!mobyle/program
name: drawtree
title: drawtree
description: Plots an unrooted tree diagram
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparameter
format: '"drawtree <drawtree.params"'
argpos: 0
name: drawtree
command: true
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
comment: Tree in Newick format.
prompt: Tree File (intree)
format: '"ln -s "+str( treefile ) + " intree && "'
simple: true
argpos: -10
mandatory: true
name: treefile
command: false
type: !mobyle/formattedtype
format_terms: ['EDAM_format:1910']
data_terms: ['EDAM_data:0872']
- !mobyle/inputprogramparameter
format: '"0\n"'
argpos: -1
paramfile: drawtree.params
name: screen_type
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: Drawtree options
name: options
children:
- !mobyle/inputprogramparameter
prompt: Which plotter or printer will the tree be drawn on
format: ("" , "P\n" + str(value) + "\n")[ value is not None and value
!= vdef ]
simple: true
argpos: 2
paramfile: drawtree.params
mandatory: true
name: plotter
command: false
type: !mobyle/stringtype
default: L
options:
- {label: PostScript printer file format (L), value: L}
- {label: PICT format (M), value: M}
- {label: HP Laserjet PCL file format (J), value: J}
- {label: MS-Windows Bitmap (W), value: W}
- {label: TeKtronix 4010 graphics terminal (K), value: K}
- {label: Hewlett-Packard pen plotter (H), value: H}
- {label: DEC ReGIS graphics (D), value: D}
- {label: Houston Instruments plotter (B), value: B}
- {label: Epson MX-80 dot-matrix printer (E), value: E}
- {label: Prowriter/Imagewriter dot-matrix printer (C), value: C}
- {label: Okidata dot-matrix printer (O), value: O}
- {label: Toshiba 24-pin dot-matrix printer (T), value: T}
- {label: PCX file format (P), value: P}
- {label: X Bitmap format (X), value: X}
- {label: FIG 2.0 format (F), value: F}
- {label: Idraw drawing program format (A), value: A}
- {label: VRML Virtual Reality Markup Language file (Z), value: Z}
- {label: POVRAY 3D rendering program file (V), value: V}
- {label: Rayshade 3D rendering program file (R), value: R}
- !mobyle/inputprogramparagraph
prompt: Bitmap options
name: bitmap_options
precond:
plotter:
'#in': [X, W]
children:
- !mobyle/inputprogramparameter
prompt: X resolution (in pixels)
format: str( value ) + "\n"
argpos: 3
paramfile: drawtree.params
mandatory: true
name: xres
command: false
type: !mobyle/integertype {default: 500}
- !mobyle/inputprogramparameter
prompt: Y resolution (in pixels)
format: str( value ) + "\n"
argpos: 4
paramfile: drawtree.params
mandatory: true
name: xyres
command: false
type: !mobyle/integertype {default: 500}
- !mobyle/inputprogramparagraph
prompt: Laserjet options
name: laserjet_options
precond: {plotter: J}
children:
- !mobyle/inputprogramparameter
prompt: Laserjet resolution
format: str(value) + "\n"
argpos: 3
paramfile: drawtree.params
mandatory: true
name: laserjet_resolution
command: false
type: !mobyle/stringtype
default: '3'
options:
- {label: 75 DPI (1), value: '1'}
- {label: 150 DPI (2), value: '2'}
- {label: 300 DPI (3), value: '3'}
- !mobyle/inputprogramparagraph
prompt: Paintbrush options
name: pcx_options
precond: {plotter: P}
children:
- !mobyle/inputprogramparameter
prompt: Paintbrush PCX resolution
format: str(value) + "\n"
argpos: 3
paramfile: drawtree.params
mandatory: true
name: pcx_resolution
command: false
type: !mobyle/stringtype
default: '3'
options:
- {label: EGA 640 X 350 (1), value: '1'}
- {label: VGA 800 X 600 (2), value: '2'}
- {label: VGA 1024 X 768 (3), value: '3'}
- !mobyle/inputprogramparagraph
prompt: POVRAY options
name: pov_options
precond: {plotter: V}
children:
- !mobyle/inputprogramparameter
format: '"Y\n"'
argpos: 2000
paramfile: drawtree.params
name: pov_validate
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: PostScript options
name: ps_options
precond: {plotter: L}
children:
- !mobyle/inputprogramparameter
prompt: Font (F)
format: ("", "F\n"+str(value)+"\n")[value is not None and value !=
vdef]
argpos: 5
paramfile: drawtree.params
name: font
command: false
type: !mobyle/stringtype
default: Times-Roman
options:
- {label: Courier, value: Courier}
- {label: Helvetica, value: Helvetica}
- {label: Helvetica-Bold, value: Helvetica-Bold}
- {label: Helvetica-BoldOblique, value: Helvetica-BoldOblique}
- {label: Helvetica-Oblique, value: Helvetica-Oblique}
- {label: Hershey, value: Hershey}
- {label: Times, value: Times}
- {label: Times-Bold, value: Times-Bold}
- {label: Times-BoldItalic, value: Times-BoldItalic}
- {label: Times-Italic, value: Times-Italic}
- {label: Times-Roman, value: Times-Roman}
- !mobyle/inputprogramparagraph
prompt: VRML options
name: vrml_options
precond: {plotter: Z}
children:
- !mobyle/inputprogramparameter
format: '"Y\n"'
argpos: 2000
paramfile: drawtree.params
name: vrml_validate
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: Rayshade options
name: ray_options
precond: {plotter: R}
children:
- !mobyle/inputprogramparameter
format: '"Y\n"'
argpos: 2000
paramfile: drawtree.params
name: ray_validate
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
format: '"V\nN\n"'
argpos: 1
paramfile: drawtree.params
name: preview
command: false
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparameter
prompt: Use branch lengths (B)
format: ("B\n" , "")[ value ]
argpos: 5
paramfile: drawtree.params
name: branch_lengths
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Angle of labels (L)
argpos: 5
paramfile: drawtree.params
name: angle
command: false
type: !mobyle/stringtype {default: M}
- !mobyle/inputprogramparameter
prompt: 'Fixed angle: Are the labels to be plotted vertically (90), horizontally
(0), or downwards (-90) (L)?'
format: ( "" , "L\nF\n"+ str( value ) +"\n")[ value is not None and value
!= vdef ]
argpos: 7
paramfile: drawtree.params
name: fixed_angle
precond:
'#or':
- {angle: ''}
- {angle: F}
command: false
type: !mobyle/floattype {default: 0.0}
- !mobyle/inputprogramparameter
prompt: Rotation of tree (in degrees from 360 to -360) (R)
format: ("" , "R\n" +str( value ) +"\n" )[ value is not None and value
!= vdef]
argpos: 5
paramfile: drawtree.params
name: rotation
command: false
type: !mobyle/floattype {default: 0.0}
- !mobyle/inputprogramparameter
prompt: Angle of arc for tree (in degrees from 0 to 360) (A)
format: ( "" , "A\n" + str( value ) +"\n" )[ value is not None and value
!= vdef]
argpos: 5
paramfile: drawtree.params
name: arc
command: false
type: !mobyle/floattype {default: 0.0}
- !mobyle/inputprogramparameter
prompt: Iterate to improve tree (I)
argpos: 5
paramfile: drawtree.params
name: iterate
command: false
type: !mobyle/stringtype {default: E}
- !mobyle/inputprogramparameter
comment: 'Default value: Automatically rescaled'
prompt: Scale of branch length (S)
format: ( "" , "S\n"+ str( value )+ "\n")[ value is not None ]
argpos: 5
paramfile: drawtree.params
name: scale
command: false
type: !mobyle/floattype {}
- !mobyle/inputprogramparameter
prompt: Try to avoid label overlap (D)
format: ( "" , "D\n" )[ value ]
argpos: 5
paramfile: drawtree.params
name: label_overlap
precond:
iterate: {'#ne': N}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Horizontal margins (M)
format: ("" , "M\n" + str( value ) + "\n" + str(vertical_margins ) + "\n")[
value is not None and value != vdef ]
argpos: 10
paramfile: drawtree.params
name: horizontal_margins
command: false
type: !mobyle/floattype {default: 1.73}
- !mobyle/inputprogramparameter
prompt: Vertical margins (M)
format: '""'
argpos: 9
paramfile: drawtree.params
name: vertical_margins
command: false
type: !mobyle/floattype {default: 2.24}
- !mobyle/inputprogramparameter
prompt: Relative character height (C)
format: ("", "C\n" + str( value ) + "\n" )[ value is not None and value
!= vdef ]
argpos: 5
paramfile: drawtree.params
name: character_height
command: false
type: !mobyle/floattype {default: 0.3333}
- !mobyle/inputprogramparameter
format: '"Y\n"'
argpos: 1000
paramfile: drawtree.params
name: confirm
command: false
hidden: true
type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparameter
prompt: Graphic tree file
filenames: '"plotfile"'
name: plotfile
precond:
plotter:
'#nin': [L, M, W, X]
- !mobyle/outputprogramparameter
prompt: Graphic tree file ( postscript format )
filenames: '"plotfile.ps"'
argpos: 10
name: psfile
precond: {plotter: L}
- !mobyle/outputprogramparameter
prompt: Graphic tree file ( pict format )
filenames: '"plotfile.pict"'
argpos: 10
name: pictfile
precond: {plotter: M}
- !mobyle/outputprogramparameter
prompt: Graphic tree file ( xbm format )
filenames: '"plotfile.xbm"'
argpos: 10
name: xbmfile
precond: {plotter: X}
- !mobyle/outputprogramparameter
prompt: Graphic tree file ( bmp format )
filenames: '"plotfile.bmp"'
argpos: 10
name: bmpfile
precond: {plotter: W}
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"drawtree.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"drawtree.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
comment: 'DRAWTREE interactively plots an unrooted tree diagram, with many options
including orientation of tree and branches, label sizes and angles, margin
sizes. Particularly if you can use your computer screen to
preview the plot, you can very effectively adjust the details of the plotting
to get just the kind of plot you want.'
operations: ['EDAM_operation:0567']
topics: ['EDAM_topics:0092', 'EDAM_topics:0084']
documentation_links: ['http://bioweb2.pasteur.fr/docs/phylip/doc/drawtree.html']
env: {}